View source: R/example_bootstrap_results.R
example_bootstrap_results | R Documentation |
Example cell type enrichment results produced by bootstrap_enrichment_test.
example_bootstrap_results(verbose = TRUE, localHub = FALSE)
verbose |
Print messages. |
localHub |
If working offline, add argument localHub=TRUE to work with a local, non-updated hub; It will only have resources available that have previously been downloaded. If offline, Please also see BiocManager vignette section on offline use to ensure proper functionality. |
List with 3 items.
# Load the single cell data
ctd <- ewceData::ctd()
# Set the parameters for the analysis
# Use 3 bootstrap lists for speed, for publishable analysis use >=10,000
reps <- 3
# Load gene list from Alzheimer's disease GWAS
example_genelist <- ewceData::example_genelist()
# Bootstrap significance test, no control for transcript length or GC content
full_results <- EWCE::bootstrap_enrichment_test( sct_data = ctd, hits = example_genelist, reps = reps, annotLevel = 1, sctSpecies = "mouse", genelistSpecies = "human" )
bootstrap_results <- full_results
save(bootstrap_results,file = "inst/extdata/bootstrap_results.rda")
full_results <- example_bootstrap_results()
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